Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions

Methods in Molecular Biology

Volumn 802, Issue , 2012, Pages 123-139

  Li, Zhiguang ^a   Kwekel, Joshua C ^a   Chen, Tao ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

Biological pathway database; Functional comparison; Gene expression; Microarray; Percentage of overlapping functions; R

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; HUMAN; INTERNET; METHODOLOGY; MOLECULAR GENETICS; RAT;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGRAMMING LANGUAGES; RATS; SOFTWARE;

EID: 84555188289     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-400-1_9     Document Type: Article

References (18)

1. Barrett JC, Kawasaki ES (2003) Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression. Drug Discov Today 8:134-141. (Pubitemid 36143983)
2. Holloway AJ, van Laar RK, Tothill RW et al (2002) Options available-from start to finish-for obtaining data from DNA microarrays II. Nat Genet 32:481-489. (Pubitemid 35435150)
3. Shi L, Reid LH, Jones WD et al (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151-1161. (Pubitemid 44359727)
4. Yauk CL, Berndt ML, Williams A et al (2004) Comprehensive comparison of six microarray technologies. Nucleic Acids Res 32:e124.
5. Tan PK, Downey TJ, Spitznagel EL Jr et al (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676-5684. (Pubitemid 37441938)
6. Barrett T, Troup DB, Wilhite SE et al (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37:D885-890.
7. Barrett T, Suzek TO, Troup DB et al (2005) NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 33:D562-566. (Pubitemid 40207937)
8. Li Z, Su Z, Wen Z et al (2009) Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. BMC Bioinformatics 10:S12.
9. Chen L, Mei N, Yao L et al (2006) Mutations induced by carcinogenic doses of aristolochic acid in kidney of Big Blue transgenic rats. Toxicol Lett 165:250-256.
10. Mei N, Arlt VM, Phillips DH et al (2006) DNA adduct formation and mutation induction by aristolochic acid in rat kidney and liver. Mutat Res 602:83-91. (Pubitemid 44693560)
11. Mengs U, Lang W, Poch J-A (1982) The carcinogenic action of aristolochic acid in rats. Archives of Toxicology 51:107-119. (Pubitemid 13202139)
12. Guo L, Lobenhofer EK, Wang C et al (2006) Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 24:1162-1169. (Pubitemid 44359728)
13. http://www.ingenuity.com/
14. http://www.r-project.org/
15. IPA. (2009) Calculating and Interpreting the p-values for Functions, Pathways, and Lists in Ingenuity Pathways Analysis. Ingenuity Systems, Redwood City, CA, 94063, USA.
16. Sun H, Fang H, Chen T et al (2006) GOFFA: gene ontology for functional analysis-a FDA gene ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics 7:S23.
17. http://cran.r-project.org/faqs.html, FAQ R.
18. http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/ default.htm, ArrayTrack.